Structure

Physi-Chem Properties

Molecular Weight:  238.19
Volume:  259.907
LogP:  3.738
LogD:  3.852
LogS:  -3.763
# Rotatable Bonds:  0
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.681
Synthetic Accessibility Score:  4.273
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.469
MDCK Permeability:  1.9707302271854132e-05
Pgp-inhibitor:  0.525
Pgp-substrate:  0.005
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.042
30% Bioavailability (F30%):  0.024

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.779
Plasma Protein Binding (PPB):  62.378082275390625%
Volume Distribution (VD):  1.055
Pgp-substrate:  35.71030044555664%

ADMET: Metabolism

CYP1A2-inhibitor:  0.053
CYP1A2-substrate:  0.273
CYP2C19-inhibitor:  0.049
CYP2C19-substrate:  0.842
CYP2C9-inhibitor:  0.043
CYP2C9-substrate:  0.124
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.151
CYP3A4-inhibitor:  0.063
CYP3A4-substrate:  0.337

ADMET: Excretion

Clearance (CL):  10.277
Half-life (T1/2):  0.42

ADMET: Toxicity

hERG Blockers:  0.047
Human Hepatotoxicity (H-HT):  0.238
Drug-inuced Liver Injury (DILI):  0.05
AMES Toxicity:  0.005
Rat Oral Acute Toxicity:  0.871
Maximum Recommended Daily Dose:  0.033
Skin Sensitization:  0.438
Carcinogencity:  0.421
Eye Corrosion:  0.982
Eye Irritation:  0.835
Respiratory Toxicity:  0.975

Download Data

Data Type Select
General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC45387

Natural Product ID:  NPC45387
Common Name*:   Ent-4Beta,10Alpha-Dihydroxyaromadendrane
IUPAC Name:   (1aS,4S,4aS,7R,7aR,7bS)-1,1,4,7-tetramethyl-1a,2,3,4a,5,6,7a,7b-octahydrocyclopropa[h]azulene-4,7-diol
Synonyms:   Ent-4Beta,10Alpha-Dihydroxyaromadendrane
Standard InCHIKey:  DWNPMJOWAWGIMM-KPRRGPHJSA-N
Standard InCHI:  InChI=1S/C15H26O2/c1-13(2)9-5-7-14(3,16)10-6-8-15(4,17)12(10)11(9)13/h9-12,16-17H,5-8H2,1-4H3/t9-,10-,11-,12-,14-,15+/m0/s1
SMILES:  CC1(C)[C@H]2CC[C@@](C)([C@H]3CC[C@](C)([C@@H]3[C@@H]12)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1774432
PubChem CID:   23424711
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0001781] Aromadendrane sesquiterpenoids
            • [CHEMONTID:0003562] 5,10-cycloaromadendrane sesquiterpenoids

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO31406 Plagiochila ovalifolia Species Plagiochilaceae Eukaryota n.a. n.a. n.a. PMID[21384863]
NPO30691 Porella chilensis Species Porellaceae Eukaryota n.a. Argentine n.a. PMID[21384863]
NPO30691 Porella chilensis Species Porellaceae Eukaryota n.a. n.a. n.a. PMID[21384863]
NPO11349 Lobophytum sp. Species Alcyoniidae Eukaryota n.a. Indonesian n.a. PMID[9584407]
NPO11349 Lobophytum sp. Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[TCMID]

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  NP Quantity Composition/Concentration

Organism ID NP ID Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  Biological Activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT83 Cell Line MCF7 Homo sapiens IC50 > 40000.0 nM PMID[492080]
NPT81 Cell Line A549 Homo sapiens IC50 > 40000.0 nM PMID[492080]
NPT306 Cell Line PC-3 Homo sapiens IC50 > 40000.0 nM PMID[492080]
NPT2 Others Unspecified Inhibition = 80.0 % PMID[492079]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa GI = 24.0 % PMID[492079]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa Inhibition = 37.0 % PMID[492079]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC45387 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
0.8824 High Similarity NPC127997
0.8824 High Similarity NPC95969
0.8571 High Similarity NPC291147
0.8276 Intermediate Similarity NPC475968
0.8246 Intermediate Similarity NPC119425
0.7966 Intermediate Similarity NPC310228
0.7966 Intermediate Similarity NPC184049
0.7966 Intermediate Similarity NPC99480
0.7966 Intermediate Similarity NPC52431
0.7903 Intermediate Similarity NPC165069
0.7742 Intermediate Similarity NPC199937
0.7167 Intermediate Similarity NPC3025
0.7143 Intermediate Similarity NPC63111
0.7077 Intermediate Similarity NPC205618
0.7077 Intermediate Similarity NPC261782
0.7077 Intermediate Similarity NPC469326
0.7031 Intermediate Similarity NPC249078
0.7031 Intermediate Similarity NPC236099
0.7031 Intermediate Similarity NPC209686
0.7 Intermediate Similarity NPC277917
0.7 Intermediate Similarity NPC178223
0.7 Intermediate Similarity NPC166894
0.7 Intermediate Similarity NPC283655
0.7 Intermediate Similarity NPC89069
0.697 Remote Similarity NPC469328
0.6957 Remote Similarity NPC471660
0.6949 Remote Similarity NPC161473
0.6909 Remote Similarity NPC77550
0.6909 Remote Similarity NPC108441
0.6901 Remote Similarity NPC139765
0.6901 Remote Similarity NPC131584
0.6875 Remote Similarity NPC185547
0.6875 Remote Similarity NPC95804
0.6842 Remote Similarity NPC294858
0.6833 Remote Similarity NPC202146
0.6833 Remote Similarity NPC32222
0.6825 Remote Similarity NPC95958
0.6774 Remote Similarity NPC150713
0.6774 Remote Similarity NPC29976
0.6765 Remote Similarity NPC474756
0.6761 Remote Similarity NPC471659
0.6712 Remote Similarity NPC188793
0.6667 Remote Similarity NPC102336
0.6667 Remote Similarity NPC66766
0.6667 Remote Similarity NPC477820
0.6667 Remote Similarity NPC128608
0.6667 Remote Similarity NPC36002
0.6667 Remote Similarity NPC117137
0.6667 Remote Similarity NPC144647
0.6615 Remote Similarity NPC15152
0.6579 Remote Similarity NPC471661
0.6579 Remote Similarity NPC473257
0.6575 Remote Similarity NPC471658
0.6571 Remote Similarity NPC471781
0.6571 Remote Similarity NPC232925
0.6571 Remote Similarity NPC63588
0.6571 Remote Similarity NPC251201
0.6567 Remote Similarity NPC243469
0.6567 Remote Similarity NPC475943
0.6567 Remote Similarity NPC190827
0.6533 Remote Similarity NPC287452
0.6533 Remote Similarity NPC269333
0.6528 Remote Similarity NPC475458
0.6528 Remote Similarity NPC304499
0.6486 Remote Similarity NPC476233
0.6479 Remote Similarity NPC41886
0.6479 Remote Similarity NPC311102
0.6471 Remote Similarity NPC328441
0.6462 Remote Similarity NPC162109
0.6462 Remote Similarity NPC475412
0.6462 Remote Similarity NPC252809
0.6438 Remote Similarity NPC155441
0.6438 Remote Similarity NPC317242
0.6429 Remote Similarity NPC66407
0.6406 Remote Similarity NPC87296
0.6406 Remote Similarity NPC475515
0.6406 Remote Similarity NPC162685
0.6406 Remote Similarity NPC215671
0.6389 Remote Similarity NPC153719
0.6389 Remote Similarity NPC470610
0.6377 Remote Similarity NPC63190
0.6364 Remote Similarity NPC216941
0.6364 Remote Similarity NPC475807
0.6351 Remote Similarity NPC142759
0.6351 Remote Similarity NPC126969
0.6351 Remote Similarity NPC115719
0.6351 Remote Similarity NPC473437
0.6351 Remote Similarity NPC163597
0.6351 Remote Similarity NPC25908
0.6351 Remote Similarity NPC141346
0.6351 Remote Similarity NPC124289
0.6338 Remote Similarity NPC254845
0.6338 Remote Similarity NPC133873
0.6324 Remote Similarity NPC300442
0.6324 Remote Similarity NPC472946
0.6308 Remote Similarity NPC469321
0.6308 Remote Similarity NPC5698
0.6301 Remote Similarity NPC48795
0.6282 Remote Similarity NPC475849
0.6282 Remote Similarity NPC475388
0.6269 Remote Similarity NPC474480
0.6267 Remote Similarity NPC185915
0.6267 Remote Similarity NPC105208
0.6267 Remote Similarity NPC128951
0.6267 Remote Similarity NPC477227
0.6267 Remote Similarity NPC192046
0.6267 Remote Similarity NPC302578
0.625 Remote Similarity NPC470071
0.625 Remote Similarity NPC252182
0.625 Remote Similarity NPC187471
0.625 Remote Similarity NPC1340
0.625 Remote Similarity NPC278550
0.625 Remote Similarity NPC471662
0.625 Remote Similarity NPC127094
0.6234 Remote Similarity NPC471656
0.6232 Remote Similarity NPC44122
0.6216 Remote Similarity NPC186851
0.6216 Remote Similarity NPC476424
0.6212 Remote Similarity NPC323153
0.6212 Remote Similarity NPC84218
0.6207 Remote Similarity NPC14552
0.6203 Remote Similarity NPC29342
0.6203 Remote Similarity NPC2572
0.6203 Remote Similarity NPC474266
0.6197 Remote Similarity NPC241085
0.6197 Remote Similarity NPC129829
0.6197 Remote Similarity NPC474900
0.6197 Remote Similarity NPC98711
0.6197 Remote Similarity NPC254037
0.6197 Remote Similarity NPC470830
0.6197 Remote Similarity NPC299948
0.619 Remote Similarity NPC471269
0.6184 Remote Similarity NPC18857
0.6184 Remote Similarity NPC471769
0.6184 Remote Similarity NPC147993
0.6184 Remote Similarity NPC471045
0.6184 Remote Similarity NPC67657
0.6176 Remote Similarity NPC69149
0.6176 Remote Similarity NPC118937
0.6176 Remote Similarity NPC159654
0.6176 Remote Similarity NPC219940
0.6176 Remote Similarity NPC281540
0.6176 Remote Similarity NPC167995
0.6173 Remote Similarity NPC64862
0.6164 Remote Similarity NPC470659
0.6164 Remote Similarity NPC470660
0.6164 Remote Similarity NPC310608
0.6154 Remote Similarity NPC469745
0.6154 Remote Similarity NPC476735
0.6143 Remote Similarity NPC136813
0.6143 Remote Similarity NPC475884
0.6143 Remote Similarity NPC473230
0.6129 Remote Similarity NPC192962
0.6125 Remote Similarity NPC242016
0.6125 Remote Similarity NPC474156
0.6111 Remote Similarity NPC192192
0.6111 Remote Similarity NPC470041
0.6104 Remote Similarity NPC476176
0.6087 Remote Similarity NPC474380
0.6087 Remote Similarity NPC238352
0.6087 Remote Similarity NPC41577
0.6087 Remote Similarity NPC61503
0.6087 Remote Similarity NPC473276
0.6087 Remote Similarity NPC477009
0.6081 Remote Similarity NPC228994
0.6081 Remote Similarity NPC10476
0.6081 Remote Similarity NPC215030
0.6081 Remote Similarity NPC192501
0.6076 Remote Similarity NPC212340
0.6066 Remote Similarity NPC474331
0.6061 Remote Similarity NPC230070
0.6061 Remote Similarity NPC87828
0.6061 Remote Similarity NPC9880
0.6056 Remote Similarity NPC472741
0.6053 Remote Similarity NPC471454
0.6029 Remote Similarity NPC211291
0.6029 Remote Similarity NPC114891
0.6029 Remote Similarity NPC133368
0.6027 Remote Similarity NPC473279
0.6027 Remote Similarity NPC195530
0.6026 Remote Similarity NPC474714
0.6 Remote Similarity NPC158208
0.6 Remote Similarity NPC243027
0.6 Remote Similarity NPC196136
0.6 Remote Similarity NPC260852
0.6 Remote Similarity NPC236588
0.5976 Remote Similarity NPC145245
0.5976 Remote Similarity NPC131365
0.5974 Remote Similarity NPC477817
0.5974 Remote Similarity NPC469324
0.5974 Remote Similarity NPC477819
0.5972 Remote Similarity NPC475062
0.597 Remote Similarity NPC135648
0.597 Remote Similarity NPC66145
0.5949 Remote Similarity NPC77311
0.5949 Remote Similarity NPC254123
0.5946 Remote Similarity NPC476422
0.5946 Remote Similarity NPC472341
0.5946 Remote Similarity NPC473238
0.5942 Remote Similarity NPC476702

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC45387 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.6909 Remote Similarity NPD386 Approved
0.6909 Remote Similarity NPD388 Approved
0.6111 Remote Similarity NPD4787 Phase 1
0.5857 Remote Similarity NPD3171 Clinical (unspecified phase)
0.5833 Remote Similarity NPD5361 Clinical (unspecified phase)
0.5833 Remote Similarity NPD5360 Phase 3
0.5823 Remote Similarity NPD6928 Phase 2
0.5821 Remote Similarity NPD3198 Approved
0.5811 Remote Similarity NPD4243 Approved
0.5789 Remote Similarity NPD3702 Approved
0.5753 Remote Similarity NPD4267 Clinical (unspecified phase)
0.5753 Remote Similarity NPD3698 Phase 2
0.5676 Remote Similarity NPD4244 Approved
0.5676 Remote Similarity NPD4245 Approved
0.5667 Remote Similarity NPD384 Approved
0.5667 Remote Similarity NPD385 Approved
0.5658 Remote Similarity NPD4785 Approved
0.5658 Remote Similarity NPD4784 Approved
0.56 Remote Similarity NPD4758 Discontinued

  Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity
B: biological targets similarity
C: networks similarity
D: cell-based bioactivity similarity
E: similarity based on clinical data